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HDBR Abnormal Fetal Samples Exome Sequencing Data

The HDBR (www.hdbr.org) is a human embryonic and fetal tissue bank supplying registered researchers with access to these valuable research materials up to 22 weeks post-conception (PCW [PMC4640175]). All of the samples collected are analysed for chromosomal abnormalities, and all samples with an abnormal phenotype are either analysed by SNP array, or exome sequenced. These datasets are generated from those abnormal samples that have been analysed by exome sequencing. To request access to this data, or if any researcher is interested in obtaining tissue from any of the samples HDBR collect, please email enquiries@hdbr.org.

Study ID EGAS00001006300

Dataset 1 - May 2022 EGAD00001008825

Exome sequencing data from seven phenotypically abnormal human fetal samples. Anaysis perfomed using Illumina NovaSeq 6000, Twist Bioscience - Human Comprehensive Exome. Paired end fastq files were aligned to hg38 reference genome using BWA-MEM v0.7.15, followed by sorting using SAMtools sort v1.3.1, and duplicate reads marked using Picard Tools MarkDuplicates v2.18.2.

Samples used:

Description	HDBR ID	Phenotype	EGA ID	Alias	Gender	Tissue used
Human fetus, 18 PCW	15832	Abnormal left hand & no right foot	EGAN00003552578	11_15832_18PCW	male	skin
Human fetus, 12 PCW	15854	Face and heart abnormal	EGAN00003552570	3_15854_12PCW	male	skin
Human fetus, 21 PCW (sample a)	15861	Cleft palate/lip	EGAN00003552579	8_15861_21PCW_A	male	skin
Human fetus, 21 PCW (sample b)	15861	Cleft palate/lip	EGAN00003552571	12_15861_21PCW_B	male	skin
Human fetus, 17 PCW (sample a)	15862	Coarctation of aorta	EGAN00003552577	2_15862_17PCW_A	male	skin
Human fetus, 17 PCW (sample b)	15862	Coarctation of aorta	EGAN00003552580	9_15862_17PCW_B	male	skin
Human fetus, 12 PCW (sample a)	15887	Retinitis pigmentosa	EGAN00003552574	5_15887_12PCW_A	female	unknown
Human fetus, 12 PCW (sample b)	15887	Retinitis pigmentosa	EGAN00003552572	6_15887_12PCW_B	female	unknown
Human fetus, 17 PCW	15922	No tibia or fibula	EGAN00003552573	7_15922_17PCW	male	skin
Human fetus, 15 PCW (sample a)	15930	Exomphalos major	EGAN00003552575	1_15930_15PCW_A	male	skin
Human fetus, 15 PCW (sample b)	15930	Exomphalos major	EGAN00003552576	10_15930_15PCW_B	male	skin

 

Dataset 2 - November 2022 EGAD00001009715

Exome sequencing data from thirteen phenotypically abnormal human fetal samples. Anaysis perfomed using Illumina NovaSeq 6000, Twist Bioscience - Human Comprehensive Exome. Paired end fastq files were aligned to hg38 reference genome using BWA-MEM v0.7.15, followed by sorting using SAMtools sort v1.3.1, and duplicate reads marked using Picard Tools MarkDuplicates v2.18.2.

Samples used:

Description	HDBR ID	Phenotype	EGA ID	Alias	Gender	Tissue used
Human fetus, 16 PCW	16382	Potential Menkes Syndrome	EGAN00004189521	44_16382_16PCW	male	skin
Human fetus, 16 PCW	16355	Cleft Palate and Aortic Bridge	EGAN00004189522	43_16355_16PCW	male	skin
Human fetus, 14 PCW	16266	Down's Syndrome	EGAN00004189523	42_16266_14PCW	male	skin
Human embryo, CS23	16050	Neural tube Defect and Cleft Palate	EGAN00004189524	41_16050_CS23	male	chorionic villi
Human fetus, 19 PCW	16191	Talipes equinovarus	EGAN00004189525	40_16191_19PCW	male	skin
Human fetus, 20 PCW	16312	Spina Bifida	EGAN00004189526	39_16312_20PCW	female	skin
Human embryo, CS19	16362	Cleft Lip and Microcephaly	EGAN00004189527	38_16362_CS19	male	skin
Human fetus, 21 PCW	16128	Cardiac Defects	EGAN00004189528	37_16128_21PCW	male	skin
Human fetus, 11 PCW	15973	Gastroschisis	EGAN00004189529	36_15973_11PCW	male	skin
Human fetus, 16 PCW	15992	Spina Bifida	EGAN00004189530	35_15992_16PCW	male	skin
Human fetus, 11 PCW	16067	Beta Thalassemia Major by Congenital Varicella Syndrome	EGAN00004189531	34_16067_11PCW	female	skin
Human fetus, 15 PCW	16012	Syndactyly and Talipes equinovarus	EGAN00004189532	33_16012_15PCW	female	skin
Human embryo, CS19	16061	Anencephaly Midbrain	EGAN00004189533	32_16061_CS19	female	limb